A crystal structure consists of an infinite three-dimensional array of
molecules and/or ions. The basic building block of this array is the
crystallographic unit cell, and the complete crystal consists of many millions
of these units.

Within the unit cell, individual molecules and ions are related to each other
in 3D space according to the symmetry of the space group. Crystal structures
can exist in any one of 230 possible space groups. Because the molecules of the
unit cell are related by symmetry only part of the cell contents, the
asymmetric unit, is required to describe the crystal structure. Frequently, but
not always (see below), the asymmetric unit is a single molecule of the
compound under study.

The example below shows the chemical diagram (a) and structural diagram (b)
for entry AADMPY10. For this entry the crystal chemical unit is the same as the
asymmetric unit. The position of the asymmetric unit in the unit cell can be
seen in (b).

(a)(b)

The space group of the crystal structure is o(P,`)1. If we denote the centroid
of the asymmetric unit by the 3D coordinates x,y,z, then the space group
symmetry will add a further two-residue asymmetric unit at :

-x, -y, -z

as shown in (c).

(c)

The positions of molecules in other unit cells can then be simply generated by
adding unit cell translations along any or all of the axial directions.

During a non-bonded search, the crystal chemical unit is used as a reference
point to search out into the extended crystal structure for intermolecular
contacts. Sometimes the crystal chemical unit will be refered to as the
reference molecule(s) when describing the operation of non-bonded commands. The
extended crystal structure that results from searching AADMPY10 for hydrogen
bonds is shown in (d). The non-bonded contacts are identified by dotted lines.
Because diagrams of the extended crystal can quickly become large and difficult
to visualize, the convention of the non-bonded search utility is to only add
the atoms necessary to represent the contact. The actual display generated by
the search is given in (e). Section 7.14.6 will provide more details about the
display of non-bonded contacts.

(d)(e)

Despite these apparent complications, all the user has to remember is that the
CSD stores coordinate data for a single asymmetric unit consisting of bonded
residues. This is known as the crystal chemical unit which is used as a
reference for non-bonded searches. The CSD also stores the symmetry operators
that are required to generate the extended crystal structure from these
reference coordinates.